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Well, a week or so ago I did my second harvest from my hive. At the time, I figures my bees were pretty much done for the season (this was before Michael Bush explained about waiting for a hard frost, etc.), so I didn't replace all the frames I removed. I think I left 6 or so.

This was the bad thing.

Last night, I went to collect the frames I had left under the outer cover for the bees to clean. I noticed that they had not only cleaned them, but started building up the cells again. (They had only been there for about 3 days!). Out of curiousity, and because of the unexpectedly high level of activity, I decided to peak under the inner cover.

!
!

It seems my bees have been busy indeed. They have much more honey. Plus, they even started building a sort of freestanding comb hanging fromt the inner cover.

So, now I don't know what to do. I figure the best thin is to wait until the frost then basically go in, remove the upper super, or whatever its called (leaving of course the two already there), taking off the queen excluder, and chase or brush the bees away from the honey chamber.

Then I can uncap the honey and try harvest even the freestanding comb, and clean the super, etc, and everything else up for next season.

I'd go straighten it out now. When it's cold is not a good time to disturb the bees. They will be clustered and very lethargic and if the cluster breaks up and falls on the bottom board they will often die there. Also if the cluster gets too cold the bees will start falling off the outside. Better when they are flying. Even if you're just thinking they will keep filling things until the frost, why not have them filling combs in frames instead of building more wild combs?

You'll need something to put the comb you're taking out (that's not in frames) in. A bowl with a lid or a clean five gallon bucket with a lid. Smoke the section that the free standing comb is in so most of the bees leave and then cut it out with a knife and lay it in the bucket or bowl. if you can lift the inner cover without it breaking off this is nice. If not, just do what you can. But get it out and put some frames back in their place. It will be a mess, just try to minimize it.

Clean it out now, before it gets out of hand. By next spring they will have moved up into the supers and the queen may be laying in the free standing comb. If you're having second thoughts on removing it now wait till you see brood or the first nector of the spring in it. It will be next fall before you have the nerve to take it out then.

The queen usually doen't make use of the burcomb under the innercover, unless its later in the spring season and she is crowded. Same goes with the bees. I think you are safe to leave it for extra winter food.
If it really bothers you, just break open all the cells and place it back on the colony over the brood nest. The bees probably will clean out the mess and store the food down below in a few days, and it leaves you free to clean up the empty comb